The U-insertion/deletion Edited Sequence Database

This database contains sequences of mitochondrial genes and cryptogenes from kinetoplastid protozoa. Edited mRNA sequences and translated amino acid sequences are also provided. The sequences are in GCG format and can be obtained as HTML files either by clicking the gene in the genomic maps, or by clicking the gene name in the Table. A novel "map" format provides the edited RNA sequence aligned with the genomic DNA sequence and the translated amino acid sequence; both U-deletions and U-insertions are indicated by gaps in the edited sequence or the genomic sequence. In the Leishmania tarentolae genomic map, the sequences of the maxicircle-encoded gRNAs are also indicated. For Trypanoplasma borreli, the sequences of the known gRNA genes encoded in the 180 kB component I DNA are provided. Alignments of nuclear rRNAs of kinetoplastids are also provided in the proper format for running phylogenetic programs.

Several alignments of gRNAs and edited mRNAs for T. brucei have been added on 4/10/98, thanks to U. Goringer.

November 26, 1999: Phytomonas serpens maxicircle sequences and a clickable map were added, thanks to D. Maslov.

May 5, 2000: Alignments of rRNA sequences from Bodonids were added thanks to D. Maslov.

Dec. 29, 2004: The codon bias table for L. tarentolae maxicircle-encoded genes was created by LS.

Jan. 1, 2005: I have posted the detailed procedure to search for gRNAs in minicircle sequences.

Oct. 16, 2007: I updated several links and added one to a technique chapter.

Feb. 11, 2011: I added an updated list of the sequences of all known proteins involved in trypanosome RNA editing.

Jan. 31, 2012: I added the L. donovani maxicircle RPS12 sequences (from D. Maslov).


Larry Simpsona,b,e, Otavio Thiemanne, Shirley Wanga, Dimitri Maslovc, and Herbert Avilad
aHoward Hughes Medical Institute, bDepartment of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA 90095-1662, and eDepartment of Medical Microbiology and Immunology, UCLA School of Medicine
cDepartment of Biology, University of California, Riverside, CA 92521
dDepartment of Biochemistry, University of Kentucky Medical Center, Lexington, Kentucky 40536-0084
e Laboratory of Protein Crystallography and Structural Biology Physics, Institute of Sao Carlos, University of Sao Paulo Av. Dr. Carlos Botelho 1465 Zip: 13560-970, PO Box: 369, Sao Carlos - SP - Brasil

We thank Paul Sloof and Rob Benne for providing the Crithidia sequences. The Phytomonas serpens sequences were provided by D. Maslov. The references are Maslov et al. (1998) and Maslov et al. (1999). The Herpetomonas CO3 sequences were kindly provided by Paul Sloof and Rob Benne from Landweber and Gilbert (1994).

Click here for a recent nomenclature convention for mitochondrial genes.

Click here for a link to the GOBASE organelle genome database.

Click here to return to the U-insertion/deletion RNA editing site.

This page created and maintained by L. Simpson